Searching journal content for articles similar to Gent et al. 23 (4): 628.

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  1. Research: miRNA-like secondary structures in maize (Zea mays) genes and transposable elements correlate with small RNAs, methylation, and expression
    • Galen T. Martin,
    • Edwin Solares,
    • Jeanelle Guadardo-Mendez,
    • Aline Muyle,
    • Alexandros Bousios,
    • and Brandon S. Gaut
    Genome Res. November 2023 33: 1932-1946; Published in Advance November 2, 2023, doi:10.1101/gr.277459.122
    ...-directed DNA methylation (RdDM) (Matzke and Mosher 2014). We predicted that miRNA-like structures should be more highly methylated because they map more smRNAs. We further predicted that this effect should be primarily detected in the CHH context, because mCHH is more dependent on RdDM than mCG and mCHG (Law...
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  2. Research: DNA methylation profiles of diverse Brachypodium distachyon align with underlying genetic diversity
    • Steven R. Eichten,
    • Tim Stuart,
    • Akanksha Srivastava,
    • Ryan Lister,
    • and Justin O. Borevitz
    Genome Res. November 2016 26: 1520-1531; Published in Advance September 9, 2016, doi:10.1101/gr.205468.116
    ...the boundary between active and repressed chromatin (Gent et al. 2013; Li et al. 2015a). As reported in maize, DTT elements are often found near genes as a common target of CHH methylation (Fig. 1D; Supplemental Fig. S5). It is certainly clear that DNA methylation patterns are often unique to specific genomic...
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  3. Research: A role for palindromic structures in the cis-region of maize Sirevirus LTRs in transposable element evolution and host epigenetic response
    • Alexandros Bousios,
    • Concepcion M. Diez,
    • Shohei Takuno,
    • Vojtech Bystry,
    • Nikos Darzentas,
    • and Brandon S. Gaut
    Genome Res. February 2016 26: 226-237; Published in Advance December 2, 2015, doi:10.1101/gr.193763.115
    ...). Symmetric methylation can be maintained and inherited to daughter DNA strands in an RdDM-independent manner, whereas CHH methylation often requires RdDM and de novo targeting (Zemach et al. 2013). Intriguingly, two recent studies have shown how a transition from post-transcriptional to transcriptional...
  4. Research: Genome-wide redistribution of 24-nt siRNAs in rice gametes
    • Chenxin Li,
    • Hengping Xu,
    • Fang-Fang Fu,
    • Scott D. Russell,
    • Venkatesan Sundaresan,
    • and Jonathan I. Gent
    Genome Res. February 2020 30: 173-184; Published in Advance January 2, 2020, doi:10.1101/gr.253674.119
    ...tissues in that mCHH was highest near genes (Fig. 3A; Supplemental Figs. S15, S16). Despite the -wide differences in distributions of 24-nt siRNAs in egg cell, sperm cell, and vegetative tissues, distributions of DNA methylation were similar between them, though the magnitude of methylation was variable...
  5. Research: Resetting of the 24-nt siRNA landscape in rice zygotes
    • Chenxin Li,
    • Jonathan I. Gent,
    • Hengping Xu,
    • Hong Fu,
    • Scott D. Russell,
    • and Venkatesan Sundaresan
    Genome Res. February 2022 32: 309-323; Published in Advance December 23, 2021, doi:10.1101/gr.275981.121
    ..., and prefertilization ovary data from Li et al. (2020).Resetting to a canonical siRNA pattern might suggest that the newly detected siRNA loci in the zygote are targeted for CHH methylation during embryogenesis in an RdDM-dependent manner. We compared DNA methylation levels across different siRNA loci categories...
  6. Research: Transcriptional activity and epigenetic regulation of transposable elements in the symbiotic fungus Rhizophagus irregularis
    • Alexandra Dallaire,
    • Bethan F. Manley,
    • Maya Wilkens,
    • Iliana Bista,
    • Clement Quan,
    • Edouard Evangelisti,
    • Charles R. Bradshaw,
    • Navin B. Ramakrishna,
    • Sebastian Schornack,
    • Falk Butter,
    • Uta Paszkowski,
    • and Eric A. Miska
    Genome Res. December 2021 31: 2290-2302; Published in Advance November 12, 2021, doi:10.1101/gr.275752.121
    ...such as CHG/CHH methylation, histone modification, or RNAi, DNA hypomethylation can lead to TE derepression. We therefore examined whether low mCG levels could be linked to TE loci expression. Indeed, members of all families of expressed TEs were significantly associated with lower mCG levels compared...
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  7. Resource: Integrated annotations and analyses of small RNA–producing loci from 47 diverse plants
    • Alice Lunardon,
    • Nathan R. Johnson,
    • Emily Hagerott,
    • Tamia Phifer,
    • Seth Polydore,
    • Ceyda Coruh,
    • and Michael J. Axtell
    Genome Res. March 2020 30: 497-513; Published in Advance March 16, 2020, doi:10.1101/gr.256750.119
    ...-directed DNA methylation (RdDM) pathway, involving 24 or 21–22 nt siRNAs. Twenty-four-nucleotide siRNAs are derived from Polymerase IV (Pol IV) transcripts that are converted to dsRNAs by RNA-dependent RNA polymerase 2 (RDR2), which are then processed by DCL3. They act in canonical RdDM, primarily targeting...
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